FIGURE 3.
Histone tails induce a natural compaction and curvature in chromatin that enhance long-range intramolecular contacts. A, simulated distributions of the end-to-end distances r (top) and radii of gyration s (bottom) of DNA chains containing 13 nucleosomes, evenly spaced by 30-bp DNA linkers and with either fully intact (native) or tailless histones (red and blue curves, respectively) when compared with those of protein-free DNA chains of the same length (black curves in insets). See supplemental Fig. S3 for the corresponding distributions with different numbers of nucleosomes. B, estimated likelihood of close (≤15 nm) contacts between NtrC and RNA polymerase-σ54 complexes bound respectively at the 3′ and 5′ ends of DNA chains with 4, 7, 13, or 25 intervening nucleosomes. Red and blue bars: native and tailless histones, respectively. C, representative configurations of chromosomal fragments bearing 25 intact (top) or tailless (bottom) nucleosomes. The DNA is represented by a color-coded backbone (progression from 5′ to 3′ ends of the DNA is depicted by the aqua to violet to magenta color sequence), and the histone cores are represented by alternating green and silver space-filled atomic representations. Images are rendered with PyMOL. See Figs. S1 and S4 for other images and curvature values.